Writes out a fresh copy of the inventory that minimizes the
amount of inventory that need be downloaded when people pull from
the repository.

Specifically, it breaks up the inventory on the most recent tag.
This speeds up most commands when run remotely, both because a
smaller file needs to be transfered (only the most recent
inventory). It also gives a guarantee that all the patches prior
to a given tag are included in that tag, so less commutation and
history traversal is needed. This latter issue can become very
important in large repositories.

Sets scripts in or below the current directory executable. A script is any file that starts
with the bytes '#!'. This is used sometimes for --set-scripts-executable, but at other times
--set-scripts-executable is handled by the hunk patch case of applyFL.

Similar to the ask function of the MonadReader class.
This allows actions in the RIO monad to get the current
repository.
FIXME: Don't export this. If we don't export this
it makes it harder for arbitrary IO actions to access
the repository and hence our code is easier to audit.